Restore proto round trip for Java DirectRunner (was: Performance degradation on the direct runner)

[kennknowles]

Running Nexmark queries with the direct runner between Beam 2.2.0 and 2.3.0 shows a performance degradation:

========================================
         Beam 2.2.0       Beam 2.3.0
  Query  Runtime(sec)
    Runtime(sec)
========================================
  0000           6.4            10.6
 
0001           5.1            10.2
  0002           3.0             5.8
  0003           3.8     
       6.2
  0004           0.9             1.4
  0005           5.8            11.4
  0006     
     0.8             1.4
  0007         193.8          1249.1
  0008           3.9             6.9

 0009           0.9             1.3
  0010           6.4             8.2
  0011           5.0    
        9.4
  0012           4.7             9.1

We can see especially Query 7 that is 10 times longer.

Imported from Jira BEAM-3617. Original Jira may contain additional context.
Reported by: jbonofre.